gwaslab 3.6.2__tar.gz → 3.6.3__tar.gz

{gwaslab-3.6.2/src/gwaslab.egg-info → gwaslab-3.6.3}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: gwaslab
-Version: 3.6.2
+Version: 3.6.3
 Summary: A collection of handy tools for GWAS SumStats
 Author-email: Yunye <gwaslab@gmail.com>
 Project-URL: Homepage, https://cloufield.github.io/gwaslab/

{gwaslab-3.6.2 → gwaslab-3.6.3}/pyproject.toml

@@ -7,7 +7,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "gwaslab"
-version = "3.6.2"
+version = "3.6.3"
 authors = [
   { name="Yunye", email="gwaslab@gmail.com" },
 ]

{gwaslab-3.6.2 → gwaslab-3.6.3}/src/gwaslab/g_Sumstats.py

@@ -102,7 +102,7 @@ from gwaslab.util_ex_run_scdrs import _run_scdrs
 #20220309
 class Sumstats():
     def __init__(self,
-             sumstats,
+             sumstats=None,
              fmt=None,
              tab_fmt="tsv",
              snpid=None,

{gwaslab-3.6.2 → gwaslab-3.6.3}/src/gwaslab/g_version.py

@@ -2,11 +2,13 @@ from gwaslab.g_Log import Log
 import subprocess
 import os
 import numpy as np 
+import sys
 
 def _show_version(log=Log(), verbose=True):
     # show version when loading sumstats
     log.write("GWASLab v{} https://cloufield.github.io/gwaslab/".format(gwaslab_info()["version"]),verbose=verbose)
     log.write("(C) 2022-2025, Yunye He, Kamatani Lab, GPL-3.0 license, gwaslab@gmail.com",verbose=verbose)
+    log.write(f"Python version: {sys.version}",verbose=verbose)
 
 def _get_version():
     # return short version string like v3.4.33
@@ -15,8 +17,8 @@ def _get_version():
 def gwaslab_info():
     # version meta information
     dic={
-   "version":"3.6.2",
-   "release_date":"20250509"
+   "version":"3.6.3",
+   "release_date":"202505"
     }
     return dic   
 

{gwaslab-3.6.2 → gwaslab-3.6.3}/src/gwaslab/io_load_ld.py

@@ -233,7 +233,9 @@ def process_ld(sumstats,
                 lead_snpid = matched_snpid.group(0).split(":")[1:]
                 lead_snpid[0]= int(lead_snpid[0])
                 lead_series = pd.Series(lead_snpid)
-
+                
+        print(sumstats)
+        print(sumstats.loc[lead_id, "REFINDEX"])
         # if lead pos is available: 
         if sumstats.loc[lead_id, "REFINDEX"] is not None:
             lead_snp_ref_index = sumstats.loc[lead_id, "REFINDEX"]

{gwaslab-3.6.2 → gwaslab-3.6.3}/src/gwaslab/io_preformat_input.py

@@ -58,7 +58,7 @@ def preformat(sumstats,
           study=None,
           trait=None,
           build=None,
-          other=[],
+          other=None,
           usekeys=None,
           chrom_pat=None,
           snpid_pat=None,
@@ -68,8 +68,10 @@ def preformat(sumstats,
 
     #renaming dictionary
     rename_dictionary = {}
-    usecols = []
-    dtype_dictionary ={}    
+    usecols = list()
+    if other is None:
+        other = list()
+    dtype_dictionary = {}    
     if readargs is None:
         readargs={}
  #######################################################################################################################################################

{gwaslab-3.6.2 → gwaslab-3.6.3}/src/gwaslab/util_ex_run_clumping.py

@@ -9,7 +9,7 @@ from gwaslab.util_ex_process_ref import _process_plink_input_files
 from gwaslab.g_version import _checking_plink_version
 
 def _clump(insumstats, vcf=None, scaled=False, out="clumping_plink2", 
-           p="P",mlog10p="MLOG10P", overwrite=False, study=None, bfile=None, 
+           p="P",mlog10p="MLOG10P", overwrite=False, study=None, bfile=None, pfile=None,
            n_cores=1, memory=None, chrom=None, clump_p1=5e-8, clump_p2=5e-8, clump_r2=0.01, clump_kb=250,
            log=Log(),verbose=True,plink="plink",plink2="plink2"):
     ##start function with col checking##########################################################
@@ -54,6 +54,7 @@ def _clump(insumstats, vcf=None, scaled=False, out="clumping_plink2",
     # process reference file
     bfile, plink_log, ref_bim,filetype = _process_plink_input_files(chrlist=sumstats["CHR"].unique(), 
                                                        bfile=bfile, 
+                                                       pfile=pfile,
                                                        vcf=vcf, 
                                                        n_cores=n_cores,
                                                        plink_log=plink_log, 
@@ -162,9 +163,12 @@ def _clump(insumstats, vcf=None, scaled=False, out="clumping_plink2",
             log.write(e.output)
         #os.system(script)
         
-        clumped = pd.read_csv("{}.clumps".format(out_single_chr),sep="\s+")
-        results = pd.concat([results,clumped],ignore_index=True)
-        
+        try:
+            clumped = pd.read_csv("{}.clumps".format(out_single_chr),sep="\s+")
+            results = pd.concat([results,clumped],ignore_index=True)
+            
+        except:
+            log.write(f"Clumping failed for chr{i}")
         # remove temp SNPIDP file 
         os.remove(clump)
     

{gwaslab-3.6.2 → gwaslab-3.6.3}/src/gwaslab/util_ex_run_scdrs.py

@@ -84,7 +84,7 @@ def _run_scdrs( scdrs="scdrs",
         bash_script+=f'''
 {python} {scdrs} perform-downstream {analysis_string} \
     --h5ad-file {h5ad_file} \
-    --score-file {trait}.full_score.gz \
+    --score-file ./{trait}.full_score.gz \
     --out-folder {out_folder} \
     --min_genes 250 \
     --min_cells 50 \

{gwaslab-3.6.2 → gwaslab-3.6.3/src/gwaslab.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: gwaslab
-Version: 3.6.2
+Version: 3.6.3
 Summary: A collection of handy tools for GWAS SumStats
 Author-email: Yunye <gwaslab@gmail.com>
 Project-URL: Homepage, https://cloufield.github.io/gwaslab/